Hello Andreas, I uncommented all tests in run-unit-test and now they work perfectly fine so I closed the bug #848326 inside changelog Also I added some info to README.test, which I think could be useful for users
Regards, Nadiya On Wed, Mar 29, 2017 at 2:48 PM, Nadiya Sitdykova <rovensk...@gmail.com> wrote: > Hello Andreas, > > >Did you do some investigation what dependency providing liblapack.so and > >libblas.so are needed (see my mail from yesterday)? > > Yes, I tried to run the test with different packages installed, and here > are results: > > packages | result | user > time > ------------------------------------------------------------ > ---------------------- > libatlas-base-dev | Successful run | 11m24.204s > libopenblas-dev | Successful run | 10m31.860s > libblas-dev+liblapack-dev | Successful run | 10m34.368s > > It seems that libatlas-base-dev is less effective, but I'm not sure if we > should exclude it from Depends, so I left if for now > > On Tue, Mar 28, 2017 at 11:29 PM, Andreas Tille <andr...@an3as.eu> wrote: > >> [Changed subject to split up to topics in one thread] >> >> Hi Nadiya, >> >> On Tue, Mar 28, 2017 at 10:23:00PM -0700, Nadiya Sitdykova wrote: >> > 1) I read the paper about mapdamage and figured out that with given >> pe.sam >> > file the reference TGAAAACGA wouldn't make sense as the particular type >> of >> > substitutions is specific for ancient DNA damages. So further for tests >> I >> > used reference CGATACGA -- which contains all types of nucleotides and >> make >> > sense regarding specifics of DNA damage. >> > >> > 2) But even after fixing (1) I still got an error (log attached). The >> > problem is that on given dataset from pe_test mapdamage produces data >> with >> > NaNs and then tries to compute quantiles on this data. I think that on >> real >> > date NaNs also could be produced, so I treated this issue as a bug and >> made >> > a patch which changes the way how quantiles are computed --- now it >> removes >> > NaNs [1] >> > >> > 3) I wrote about all this to upstream as a comments to earlier created >> > issue and asked if it's really was a bug in their opinion >> > >> > 4) FInally, move forward to fixing mapdamage test suite >> >> Pretty good job. That's exactly the contribution I'm envisioning for the >> Outreachy project. I've just added the URL of the upstream issue to the >> patch. >> >> > 11: stop("missing values and NaN's not allowed if 'na.rm' is FALSE") >> > 10: quantile.default(newX[, i], ...) >> > 9: FUN(newX[, i], ...) >> > 8: apply(X, 1, quantile, c(0.025)) >> > 7: data.frame(x = 1:nrow(da), pos = da[, "Pos"], mea = apply(X, >> > 1, mean), med = apply(X, 1, median), loCI = apply(X, 1, quantile, >> > c(0.025)), hiCI = apply(X, 1, quantile, c(0.975))) >> > 6: calcSampleStats(da, CTs) >> > 5: postPredCheck(dat, mcmcOut) >> > 4: eval(expr, envir, enclos) >> > 3: eval(ei, envir) >> > 2: withVisible(eval(ei, envir)) >> > 1: source(paste(path_to_mapDamage_stats, "main.R", sep = "")) >> > The Bayesian statistics program failed to finish >> > Traceback (most recent call last): >> > File "/usr/local/bin/mapDamage", line 382, in <module> >> > sys.exit(main()) >> > File "/usr/local/bin/mapDamage", line 365, in main >> > mapdamage.rscript.run_stats(options) >> > File "/usr/local/lib/python2.7/dist-packages/mapdamage/rscript.py", >> line 144, in run_stats >> > raise e >> > subprocess.CalledProcessError: Command '['Rscript', >> '/usr/local/lib/python2.7/dist-packages/mapdamage/Rscripts/stats/runGeneral.R', >> '--args', '30', '10000', '10', '50000', '0', '0', '1', '1', '0', '0', '1', >> '12', 'results_pe/', '/usr/local/lib/python2.7/dist >> -packages/mapdamage/Rscripts/stats/', 'results_pe/Stats_out', '0', '0', >> '0', 'results_pe/acgt_ratio.csv', '0', '0']' returned non-zero exit status 1 >> >> I'd recommend to manually run this script. >> >> Did you do some investigation what dependency providing liblapack.so and >> libblas.so are needed (see my mail from yesterday)? >> >> Kind regards >> >> Andreas. >> >> -- >> http://fam-tille.de >> >> >